Previously I have been running a command like this:
java -jar /path/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-R /path/human_g1k_v37.fasta \
-et NO_ET \
-K /path/key \
-out_mode EMIT_ALL_SITES \
--input_file /path/bam \
-L /path/intervals \
-gt_mode GENOTYPE_GIVEN_ALLELES \
--alleles /path/vcf \
--dbsnp /path/dbsnp_135.b37.vcf \
-o /path/my.vcf
But I was reading the documentation again and I read this statement: GENOTYPE_GIVEN_ALLELES only the alleles passed in from a VCF rod bound to the -alleles argument will be used for genotyping
Which lead me to believe that there wasn't a need to include the lines: --input_file /path/bam \ -L /path/intervals \
because it would be redundant. But when I try to run without those line I get back an error message: Walker requires reads but none were provided.
Can you give an explaination as to why both of those lines AND GENOTYPE_GIVEN_ALLELES would be needed?